changes while testing

[mothur.git] / decalc.h

diff --git a/decalc.h b/decalc.h
index e2a6cc78c10a9048facef623a322010a3c85bd12..d1daf050e004333228e39fb5aaa7621dd1b0bcf6 100644 (file)
--- a/decalc.h
+++ b/decalc.h
@@ -14,7 +14,7 @@
 
 /***********************************************************************/
 
-//This class was created using the algorythms described in the 
+//This class was created using the algorithms described in the 
 // "At Least 1 in 20 16S rRNA Sequence Records Currently Held in the Public Repositories is Estimated To Contain Substantial Anomalies" paper 
 //by Kevin E. Ashelford 1, Nadia A. Chuzhanova 3, John C. Fry 1, Antonia J. Jones 2 and Andrew J. Weightman 1.
 
@@ -36,15 +36,18 @@ class DeCalculator {
 
        public:
                
-               DeCalculator() {};
+               DeCalculator() { m = MothurOut::getInstance(); }
                ~DeCalculator() {};
                
+               vector<Sequence> findClosest(Sequence, vector<Sequence*>&, vector<Sequence*>&, int, int);  //takes querySeq, a reference db, filteredRefDB, numWanted, minSim 
+               Sequence* findClosest(Sequence*, vector<Sequence*>);
                set<int> getPos() {  return h;  }
                void setMask(string); 
                void setAlignmentLength(int l) {  alignLength = l;  }
                void runMask(Sequence*);
                void trimSeqs(Sequence*, Sequence*, map<int, int>&);
-               vector< vector<float> > removeObviousOutliers(vector< vector<quanMember> >&, int);
+               map<int, int> trimSeqs(Sequence&, vector<Sequence>&);
+               void removeObviousOutliers(vector< vector<float> >&, int);
                vector<float> calcFreq(vector<Sequence*>, string);
                vector<int> findWindows(Sequence*, int, int, int&, int);
                vector<float> calcObserved(Sequence*, Sequence*, vector<int>, int);
@@ -53,18 +56,22 @@ class DeCalculator {
                float calcDE(vector<float>, vector<float>);
                float calcDist(Sequence*, Sequence*, int, int);
                float getCoef(vector<float>, vector<float>);
-               vector< vector<quanMember> > getQuantiles(vector<Sequence*>, vector<int>, int, vector<float>, int, int, int, vector<float>&);
+               vector< vector<float> > getQuantiles(vector<Sequence*>, vector<int>, int, vector<float>, int, int, int);
                
                vector<int> returnObviousOutliers(vector< vector<quanMember> >, int);
                
+               map<int, int> getMaskMap() { return maskMap; }
+               
        private:
-               vector<quanMember> sortContrib(map<quanMember*, float>);  //used by mallard
+               //vector<quanMember> sortContrib(map<quanMember*, float>);  //used by mallard
                float findAverage(vector<float>);
                //int findLargestContrib(vector<int>);
                //void removeContrib(int, vector<quanMember>&);
                string seqMask;
                set<int> h;
                int alignLength;
+               map<int, int> maskMap;
+               MothurOut* m;
 
 };